Bacterial SNPs calling with both Illumina short reads and nanopore long reads

Question

[lynnchen31]

Hi
I have 30 bacterial genomes with both Illumina short reads and nanopore long reads, which I got high quality assembly from them. Now I want to call SNPs of the 30 genomes, so I could use this SNPs data for association analysis with phenotype. So far the available SNP caller I know for bacteria are CFSAN, NASP, SNIPPY, PHENix, BactSNP. Now my question is: how do I know which SNP caller to use? can use both short and long reads fastq data? why none of them recoomend fasta file as input?

Thanks, Best,